The Dependency Map (DepMap) is a genome-wide pooled CRISPR-Cas9 knockout proliferation screen conducted in more than 700 cancer cell lines spanning many different tumor lineages. Each cell line in the DepMap contains a unique barcode, and each gene knockout is assigned a “dependency score” on a per cell-line basis. The dependency score quantifies the rate of CRISPR-Cas9 guide drop out for each guide in each cell line. It has been found that proteins with similar DepMap scores across cell lines, a phenomenon known as co-dependent genes, have closely related biological functions. This can include activity in the same or parallel pathways or membership in the same protein complex or the same pathway.
We identified the strongest seven co-dependent genes for DUBs and ran GO enrichment analysis in order to explore the pathways and complexes DUBs are correlated with in the DepMap. We sought to provide support for the co-dependent genes being in the same pathway or complex by leveraging additional datasets. We used BioGRID, IntAct, and Pathway Commons PPIDs, and the NURSA PPID to determine whether co-dependent genes interact with one another. As another approach to identify potential interactors, we looked at proteomics data from the Broad Institute's Cancer Cell Line Encyclopedia (CCLE) for proteins whose expression across ~375 cell lines strongly correlated with the abundance of each DUB; it has previously been observed that proteins in the same complex are frequently significantly co-expressed. And, we determined whether co-dependent genes yield similar transcriptomic signatures in the Broad Institute's Connectivity Map (CMap).
| Symbol | Name | DepMap Correlation | Evidence | CCLE Correlation | CCLE Z-score | CCLE p-value (adj) | CCLE Significant | CMAP Score | CMAP Type |
|---|---|---|---|---|---|---|---|---|---|
| N4BP1 | NEDD4 binding protein 1 | 0.466 | 0.32 | 1.69 | 1.40e-07 | ||||
| TRAF3 | TNF receptor associated factor 3 | 0.383 | INDRA | 0.11 | 0.53 | 1.36e-01 | 99.44 | kd | |
| NFKBIA | NFKB inhibitor alpha | 0.283 | INDRA | 0.14 | 0.66 | 1.22e-01 | 90.25 | oe | |
| TNFAIP3 | TNF alpha induced protein 3 | 0.272 | INDRA | 0.14 | 0.66 | 7.05e-02 | -94.74 | oe | |
| TRAF2 | TNF receptor associated factor 2 | 0.242 | BioGRID Pathway Commons INDRA | 0.25 | 1.30 | 6.91e-05 | 99.91 | oe | |
| BCL10 | BCL10 immune signaling adaptor | -0.233 | 0.24 | 1.21 | 2.22e-04 | 99.95 | oe | ||
| CHUK | component of inhibitor of nuclear factor kappa B kinase complex | -0.231 | 0.27 | 1.38 | 2.23e-05 |
Gene set enrichment analysis was done on the genes correlated with CYLDusing the terms from Gene Ontology and gene sets derived from theGene Ontology Annotations database via MSigDB.
Using the biological processes and other Gene Ontology terms from well characterized DUBs as a positive control, several gene set enrichment analyses were considered. Threshold-less methods like GSEA had relatively poor results. Over-representation analysis with a threshold of of the top 7 highest absolute value Dependency Map correlations yielded the best results and is reported below.
The following table shows the significantly differentially expressed genes after knocking down CYLD.
| Symbol | Name | log2-fold-change | p-value | p-value (adj.) |
|---|---|---|---|---|
| BIRC3 | baculoviral IAP repeat containing 3 | 1.01e+00 | 1.57e-18 | 1.99e-14 |
| CXCL8 | C-X-C motif chemokine ligand 8 | 1.49e+00 | 3.06e-17 | 1.94e-13 |
| CSF2 | colony stimulating factor 2 | 1.20e+00 | 5.02e-16 | 2.12e-12 |
| CXCL2 | C-X-C motif chemokine ligand 2 | 1.27e+00 | 5.83e-10 | 1.73e-06 |
| CXCL3 | C-X-C motif chemokine ligand 3 | 1.34e+00 | 7.57e-10 | 1.73e-06 |
| LAMC2 | laminin subunit gamma 2 | 9.68e-01 | 8.20e-10 | 1.73e-06 |
| SOD2 | superoxide dismutase 2 | 6.95e-01 | 1.04e-09 | 1.88e-06 |
| G0S2 | G0/G1 switch 2 | 4.73e-01 | 1.74e-09 | 2.76e-06 |
| CXCL1 | C-X-C motif chemokine ligand 1 | 1.10e+00 | 2.19e-09 | 3.08e-06 |
| MMP1 | matrix metallopeptidase 1 | 4.45e-01 | 4.90e-09 | 6.20e-06 |
| IL1B | interleukin 1 beta | 1.34e+00 | 7.86e-09 | 9.04e-06 |
| TNFSF15 | TNF superfamily member 15 | 9.28e-01 | 9.39e-09 | 9.90e-06 |
| C15orf48 | chromosome 15 open reading frame 48 | 7.19e-01 | 1.07e-08 | 1.04e-05 |
| ICAM1 | intercellular adhesion molecule 1 | 1.00e+00 | 4.30e-08 | 3.89e-05 |
| NAMPT | nicotinamide phosphoribosyltransferase | 5.70e-01 | 4.62e-08 | 3.90e-05 |
| TFPI2 | tissue factor pathway inhibitor 2 | 7.05e-01 | 6.85e-08 | 5.42e-05 |
| CSF3 | colony stimulating factor 3 | 1.29e+00 | 1.41e-07 | 1.05e-04 |
| PTX3 | pentraxin 3 | 6.63e-01 | 2.45e-07 | 1.73e-04 |
| SYNGR2 | synaptogyrin 2 | 6.75e-01 | 7.33e-07 | 4.88e-04 |
| NFKBIA | NFKB inhibitor alpha | 5.70e-01 | 3.07e-06 | 1.94e-03 |
| KYNU | kynureninase | 7.62e-01 | 1.35e-05 | 8.13e-03 |
| DUSP28 | dual specificity phosphatase 28 | 9.38e-01 | 2.31e-05 | 1.33e-02 |
| AKR1B1 | aldo-keto reductase family 1 member B | 3.56e-01 | 2.97e-05 | 1.63e-02 |
| SERPIND1 | serpin family D member 1 | 7.78e-01 | 4.99e-05 | 2.63e-02 |
| CD44 | CD44 molecule (Indian blood group) | 3.75e-01 | 5.72e-05 | 2.89e-02 |
| IL6 | interleukin 6 | 7.86e-01 | 7.26e-05 | 3.54e-02 |
| SAA2 | serum amyloid A2 | 5.76e-01 | 1.10e-04 | 4.99e-02 |
| SQSTM1 | sequestosome 1 | 4.96e-01 | 1.09e-04 | 4.99e-02 |